UAE airports "use the most sophisticated security check systems … which are applied to all travellers without exception and do not target a particular nationality," the state WAM news agency quoted a foreign ministry official as saying.
The Iranian foreign ministry said on Tuesday that it had summoned the UAE's charge d'affaires in Tehran to deliver a "strong protest against the insulting and discriminatory behaviour of this country's airport officials towards our citizens."
In a statement carried by the Fars news agency, the ministry accused airport officials of "creating unusual problems for Iranians" and arresting some of them.
The Emirati foreign ministry official voiced "surprise" at Iran's failure to pinpoint the alleged cases of discrimination and said authorities were prepared to look into any specific complaint by any traveller.
Much of Iran's foreign trade passes through the UAE which has an Iranian expatriate population of some 450,000.
The row over the UAE's treatment of Iranians came amid a renewed war of words between the two governments over the strategic islands of Abu Musa and the Greater and Lesser Tunbs.
Tehran's establishment last month of a maritime rescue office and a ship registration office on Abu Musa — the only one of the three islands which is inhabited — drew a formal UAE protest.
